Package 'drugTargetInteractions' reference manual

Title:	Drug-Target Interactions
Description:	Provides utilities for identifying drug-target interactions for sets of small molecule or gene/protein identifiers. The required drug-target interaction information is obained from a local SQLite instance of the ChEMBL database. ChEMBL has been chosen for this purpose, because it provides one of the most comprehensive and best annotatated knowledge resources for drug-target information available in the public domain.
Authors:	Thomas Girke [cre, aut]
Maintainer:	Thomas Girke <[email protected]>
License:	Artistic-2.0
Version:	1.15.0
Built:	2024-11-30 05:52:18 UTC
Source:	https://github.com/bioc/drugTargetInteractions

Drug-Target Interactions

Description

The drugTargetInteractions package provides utilities for identifying drug-target interactions for sets of small molecule or gene/protein identifiers. The required drug-target interaction information is obained from a local SQLite instance of the ChEMBL database.

Details

The DESCRIPTION file:

Package:	drugTargetInteractions
Type:	Package
Title:	Drug-Target Interactions
Version:	1.15.0
Date:	2023-10-24
Authors@R:	person("Thomas", "Girke", email="[email protected]", role=c("cre", "aut"))
Description:	Provides utilities for identifying drug-target interactions for sets of small molecule or gene/protein identifiers. The required drug-target interaction information is obained from a local SQLite instance of the ChEMBL database. ChEMBL has been chosen for this purpose, because it provides one of the most comprehensive and best annotatated knowledge resources for drug-target information available in the public domain.
Depends:	methods, R (>= 4.1)
Imports:	utils, RSQLite, UniProt.ws, biomaRt,ensembldb, BiocFileCache,dplyr,rappdirs, AnnotationFilter, S4Vectors
Suggests:	RUnit, BiocStyle, knitr, rmarkdown, ggplot2, reshape2, DT, EnsDb.Hsapiens.v86
VignetteBuilder:	knitr
License:	Artistic-2.0
NeedsCompilation:	no
URL:	https://github.com/girke-lab/drugTargetInteractions
biocViews:	Cheminformatics, BiomedicalInformatics, Pharmacogenetics, Pharmacogenomics, Proteomics, Metabolomics
RoxygenNote:	7.1.1
BugReports:	https://github.com/girke-lab/drugTargetInteractions
Config/pak/sysreqs:	make libicu-dev libpng-dev libxml2-dev libssl-dev
Repository:	https://bioc.r-universe.dev
RemoteUrl:	https://github.com/bioc/drugTargetInteractions
RemoteRef:	HEAD
RemoteSha:	262cba990e3a34e7f0a5c0ddc4e8567950179116
Author:	Thomas Girke [cre, aut]
Maintainer:	Thomas Girke <[email protected]>

Index of help topics:

cmpIdMapping            cmpIdMapping
downloadChemblDb        downloadChemblDb
downloadUniChem         downloadUniChem
drugTargetAnnot         drugTargetAnnot
drugTargetAnnotTable    drugTargetAnnotTable
drugTargetBioactivity   drugTargetBioactivity
drugTargetInteractions-package
                        Drug-Target Interactions
genConfig               genConfig
getDrugTarget           getDrugTarget
getParalogs             getParalogs
getSymEnsUp             Gene to Protein ID Mappings
getUniprotIDs           Retrieve UniProt IDs via ID and Cluster
                        Mappings
processDrugage          processDrugage
runDrugTarget_Annot_Bioassay
                        runDrugTarget_Annot_Bioassay
transformTTD            transformTTD

Author(s)

Thomas Girke [cre, aut]

Maintainer: Thomas Girke <[email protected]>

cmpIdMapping

Description

Function to generate compound ID mappings UniChem.

This function requires the ID mapping files "src1src2.txt.gz", "src1src22.txt.gz", and "src1src7.txt.gz" to exist in a directory called "downloads" before being run. These can be generated with the downloadUniChem function.

It will do some processing on these files and output an RDS file at outfile. This file can then be used in other functions, such as drugTargetAnnot.

Usage

cmpIdMapping(outfile=file.path(config$resultsPath,"cmp_ids.rds"), rerun=TRUE,config=genConfig()) 
cmpIdMapping(outfile=file.path(config$resultsPath,"cmp_ids.rds"), rerun=TRUE,config=genConfig())

Arguments

`outfile`	Path to output file.
`rerun`	If true, runs processing, otherwise does nothing.
`config`	General configuration. See `genConfig`.

Value

Generates an RDS file at outfile.

Author(s)

Thomas Girke

Examples

	 
	 cmpIdMapping("cmp_ids.rds",rerun=FALSE)
cmpIdMapping("cmp_ids.rds",rerun=FALSE)

downloadChemblDb

Description

Download ChEMBL sqlite db for use by several other functions in the package.

Usage


downloadChemblDb(version,rerun=TRUE,config=genConfig())
downloadChemblDb(version,rerun=TRUE,config=genConfig())

Arguments

`version`	The ChEMBL version to download.
`rerun`	If TRUE, the file will be downloaded, otherwise do nothing.
`config`	The configuration object. This gives the location to put the downloaded chembl db.

Value

No return value.

Author(s)

Kevin Horan

Examples

	
		downloadChemblDb(27)
	
downloadChemblDb(27)

downloadUniChem

Description

Downloads UniChem compound ID mappings from https://www.ebi.ac.uk/unichem/ucquery/listSources. Mappings are downloaded for DrugBank, PubChem, and ChEBI.

Usage

downloadUniChem(rerun=TRUE, config=genConfig())
downloadUniChem(rerun=TRUE, config=genConfig())

Arguments

`rerun`	If true, downloads the files, else does nothing.
`config`	General configuration. See `genConfig`.

Value

Generates the following output files: "src1src2.txt.gz", "src1src22.txt.gz", and "src1src7.txt.gz". These correspond to mappings from ChEMBL to DrugBank, PubChem, and ChEBI, respectivly.

Author(s)

Thomas Girke

References

https://www.ebi.ac.uk/unichem/ucquery/listSources

Examples

	downloadUniChem(rerun=TRUE)
downloadUniChem(rerun=TRUE)

drugTargetAnnot

Description

Function to query known drug-target annotations.

Usage

drugTargetAnnot(queryBy=list(molType=NULL, idType=NULL, ids=NULL), cmpid_file=file.path(config$resultsPath,"cmp_ids.rds"), config=genConfig())
drugTargetAnnot(queryBy=list(molType=NULL, idType=NULL, ids=NULL), cmpid_file=file.path(config$resultsPath,"cmp_ids.rds"), config=genConfig())

Arguments

`queryBy`	A list defining the query, as described in `queryBy`.
`cmpid_file`	Path to a compound ID mapping file, generated by `cmpIdMapping`.
`config`	General configuration. See `genConfig`.

Value

Returns the query results as a data frame.

Author(s)

Thomas Girke

Examples

	
	# Tthese are just sample files included in the package. 
	# You should use your own data files.
	config = genConfig(chemblDbPath= 
									system.file("extdata", "chembl_sample.db", package="drugTargetInteractions"),
							  resultsPath = 
									system.file("extdata", "results", package="drugTargetInteractions"))

	queryBy <- list(molType="cmp", idType="chembl_id", ids=c("CHEMBL1233058", "CHEMBL1200916", "CHEMBL437765"))
	qresult <- drugTargetAnnot(queryBy, config=config)
# Tthese are just sample files included in the package. 
	# You should use your own data files.
	config = genConfig(chemblDbPath= 
									system.file("extdata", "chembl_sample.db", package="drugTargetInteractions"),
							  resultsPath = 
									system.file("extdata", "results", package="drugTargetInteractions"))

	queryBy <- list(molType="cmp", idType="chembl_id", ids=c("CHEMBL1233058", "CHEMBL1200916", "CHEMBL437765"))
	qresult <- drugTargetAnnot(queryBy, config=config)

drugTargetAnnotTable

Description

Generates a drug target annotation TSV file. This file includes target information from ChEMBL, drugbank, pubchem, and chembi.

Usage

drugTargetAnnotTable(outfile, rerun=TRUE,config=genConfig()) 
drugTargetAnnotTable(outfile, rerun=TRUE,config=genConfig())

Arguments

`outfile`	The name of the output file to write the results to.
`rerun`	If true, download and generate output file. Otherwise do nothing.
`config`	General configuration. See `genConfig`.

Value

Writes output file to outfile.

Author(s)

Thomas Girke

Examples

	config = genConfig(chemblDbPath= 
					system.file("extdata", "chembl_sample.db", package="drugTargetInteractions"))
	drugTargetAnnotTable(outfile="drugTargetAnnot.xls", config=config)

config = genConfig(chemblDbPath= 
					system.file("extdata", "chembl_sample.db", package="drugTargetInteractions"))
	drugTargetAnnotTable(outfile="drugTargetAnnot.xls", config=config)

drugTargetBioactivity

Description

Function to query bioactivity data by target or compound ids

Usage

drugTargetBioactivity( queryBy=list(molType=NULL, idType=NULL, ids=NULL), cmpid_file=file.path(config$resultsPath,"cmp_ids.rds"),config=genConfig()) 
drugTargetBioactivity( queryBy=list(molType=NULL, idType=NULL, ids=NULL), cmpid_file=file.path(config$resultsPath,"cmp_ids.rds"),config=genConfig())

Arguments

`queryBy`	A list defining the query, as described in `queryBy`.
`cmpid_file`	Path to a compound ID mapping file, generated by `cmpIdMapping`.
`config`	General configuration. See `genConfig`.

Value

Returns results as a data frame.

Author(s)

Thomas Girke

Examples

		 config = genConfig(chemblDbPath= 
										system.file("extdata", "chembl_sample.db", package="drugTargetInteractions"),
								  resultsPath = 
										system.file("extdata", "results", package="drugTargetInteractions"))

		 queryBy <- list(molType="protein", idType="uniprot", ids=c("P05979", "P35354", "P33033", "Q8VCT3", "P29475", "P51511"))
		 qresult <- drugTargetBioactivity( queryBy, config=config)

		 queryBy <- list(molType="cmp", idType="molregno", ids=c("101036", "101137", "1384464")) 
		 qresult <- drugTargetBioactivity( queryBy, config=config)

		 queryBy <- list(molType="cmp", idType="DrugBank_ID", ids=c("DB00945", "DB00316", "DB01050")) 
		 qresult <- drugTargetBioactivity(queryBy, config=config)

		 queryBy <- list(molType="cmp", idType="PubChem_ID", ids=c("2244", "3672", "1983")) 
		 qresult <- drugTargetBioactivity(queryBy, config=config)


config = genConfig(chemblDbPath= 
										system.file("extdata", "chembl_sample.db", package="drugTargetInteractions"),
								  resultsPath = 
										system.file("extdata", "results", package="drugTargetInteractions"))

		 queryBy <- list(molType="protein", idType="uniprot", ids=c("P05979", "P35354", "P33033", "Q8VCT3", "P29475", "P51511"))
		 qresult <- drugTargetBioactivity( queryBy, config=config)

		 queryBy <- list(molType="cmp", idType="molregno", ids=c("101036", "101137", "1384464")) 
		 qresult <- drugTargetBioactivity( queryBy, config=config)

		 queryBy <- list(molType="cmp", idType="DrugBank_ID", ids=c("DB00945", "DB00316", "DB01050")) 
		 qresult <- drugTargetBioactivity(queryBy, config=config)

		 queryBy <- list(molType="cmp", idType="PubChem_ID", ids=c("2244", "3672", "1983")) 
		 qresult <- drugTargetBioactivity(queryBy, config=config)

genConfig

Description

Create a default configuration object.

Usage


genConfig( chemblDbPath = "chembldb.db", downloadPath = "downloads", resultsPath = "results" )
genConfig( chemblDbPath = "chembldb.db", downloadPath = "downloads", resultsPath = "results" )

Arguments

`chemblDbPath`	Path or filename of ChEMBL SQLite db file.
`downloadPath`	The name of a directory to put downloaded files in.
`resultsPath`	The name of a directory to put output files in.

Value

A config object that can be passed to ther functions.

Author(s)

Kevin Horan

Examples

	config = genConfig()
config = genConfig()

getDrugTarget

Description

This function allows you to query a subset of the data fetched by drugTargetAnnotTable.

Usage

getDrugTarget(dt_file=file.path(config$resultsPath,"drugTargetAnnot.xls"), queryBy=list(molType=NULL, idType=NULL, ids=NULL), 
								  id_mapping=c(chembl="chembl_id", pubchem="PubChem_ID", uniprot="UniProt_ID"), columns,config=genConfig()) 
getDrugTarget(dt_file=file.path(config$resultsPath,"drugTargetAnnot.xls"), queryBy=list(molType=NULL, idType=NULL, ids=NULL), 
								  id_mapping=c(chembl="chembl_id", pubchem="PubChem_ID", uniprot="UniProt_ID"), columns,config=genConfig())

Arguments

`dt_file`	The drug target annotation file. This can be generated with `drugTargetAnnotTable`.
`queryBy`	A list defining the query, as described in `queryBy`.
`id_mapping`	A list providing the id columns for ChEMBL, PubChem, and UniProt. It should contain the fields "chembl", "pubchem", and "uniprot", each wit the column name of the respective id number in the drug target annotation file. See default value above for an example.
`columns`	A list of column indexes to select as a subset of the final result set.
`config`	General configuration. See `genConfig`.

Value

Returns the query result as a data frame.

Author(s)

Thomas Girke

Examples



		 config = genConfig(chemblDbPath= 
									system.file("extdata", "chembl_sample.db", package="drugTargetInteractions"),
							  resultsPath = 
									system.file("extdata", "results", package="drugTargetInteractions"))
		 id_mapping <- c(chembl="chembl_id", pubchem="PubChem_ID", uniprot="UniProt_ID", drugbank="DrugBank_ID")

		 queryBy <- list(molType="cmp", idType="chembl", ids=c("CHEMBL25", "CHEMBL1742471"))
		 getDrugTarget(queryBy=queryBy, id_mapping=id_mapping,
								 columns=c(1,5,8,16,17),config=config) 

		 queryBy <- list(molType="cmp", idType="pubchem", ids=c("2244", "65869", "2244"))
		 getDrugTarget(queryBy=queryBy, id_mapping=id_mapping,
								 columns=c(1,5,8,16,17),config=config) 

		 queryBy <- list(molType="protein", idType="uniprot", ids=c("P43166", "P00915", "P43166"))
		 getDrugTarget(queryBy=queryBy, id_mapping=id_mapping,
								 columns=c(1,5,8,16,17),config=config)

config = genConfig(chemblDbPath= 
									system.file("extdata", "chembl_sample.db", package="drugTargetInteractions"),
							  resultsPath = 
									system.file("extdata", "results", package="drugTargetInteractions"))
		 id_mapping <- c(chembl="chembl_id", pubchem="PubChem_ID", uniprot="UniProt_ID", drugbank="DrugBank_ID")

		 queryBy <- list(molType="cmp", idType="chembl", ids=c("CHEMBL25", "CHEMBL1742471"))
		 getDrugTarget(queryBy=queryBy, id_mapping=id_mapping,
								 columns=c(1,5,8,16,17),config=config) 

		 queryBy <- list(molType="cmp", idType="pubchem", ids=c("2244", "65869", "2244"))
		 getDrugTarget(queryBy=queryBy, id_mapping=id_mapping,
								 columns=c(1,5,8,16,17),config=config) 

		 queryBy <- list(molType="protein", idType="uniprot", ids=c("P43166", "P00915", "P43166"))
		 getDrugTarget(queryBy=queryBy, id_mapping=id_mapping,
								 columns=c(1,5,8,16,17),config=config)

getParalogs

Description

Using biomaRt, obtain for query genes the corresponding UniProt IDs as well as paralogs. Query genes can be Gene Names or ENSEMBL Gene IDs from H sapiens. The result is similar to IDMs and SSNNs from getUniprotIDs function, but instead of UNIREF clusters, biomaRt's paralogs are used to obtain SSNNs.

Usage

getParalogs(queryBy)
getParalogs(queryBy)

Arguments

queryBy

A list defining the query, as described in queryBy.

Value

Returns a list with the paralogs for the given genes.

Author(s)

Thomas Girke

Examples

	 queryBy <- list(molType="gene", idType="external_gene_name", ids=c("ZPBP", "MAPK1", "EGFR"))
	 
		 #requires network connection and is slow
		 result <- getParalogs(queryBy)
	 
queryBy <- list(molType="gene", idType="external_gene_name", ids=c("ZPBP", "MAPK1", "EGFR"))
	 
		 #requires network connection and is slow
		 result <- getParalogs(queryBy)

Gene to Protein ID Mappings

Description

The getSymEnsUp function returns for a query of gene or protein IDs a mapping table containing: ENSEMBL Gene IDs, Gene Names/Symbols, UniProt IDs and ENSEMBL Protein IDs. Subsequent slots contain the corresponding named character vectors. Internally, the function uses the ensembldb package.

Usage

getSymEnsUp(EnsDb = "EnsDb.Hsapiens.v86", ids, idtype)
getSymEnsUp(EnsDb = "EnsDb.Hsapiens.v86", ids, idtype)

Arguments

`EnsDb`	`EnsDb` instance of ensembldb package
`ids`	Character vector with IDs matching the type specified under `idtype`
`idtype`	Character vector of length one containing one of: `GENE_NAME`, `ENSEMBL_GENE_ID` or `UNIPROT_ID`

Value

List object with following components:

`idDF`	ID mapping `data.frame`
`ens_gene_id`	named character vector
`up_ens_id`	named character vector
`up_gene_id`	named character vector

Author(s)

Thomas Girke

Examples

	 gene_name <- c("CA7", "CFTR")
	 getSymEnsUp(EnsDb="EnsDb.Hsapiens.v86", ids=gene_name, idtype="GENE_NAME")
gene_name <- c("CA7", "CFTR")
	 getSymEnsUp(EnsDb="EnsDb.Hsapiens.v86", ids=gene_name, idtype="GENE_NAME")

Retrieve UniProt IDs via ID and Cluster Mappings

Description

The following returns for a set of query IDs (e.g. Ensembl gene IDs) the corresponding UniProt IDs based on two independent approaches: ID mappings (IDMs) and sequence similarity nearest neighbors (SSNNs) using UNIREF clusters. Note, the 'keys' or query IDs (e.g. ENSEMBL genes) can only be reliably maintained in the SSNN results when 'chunksize=1' since batch queries for protein clusters with 'UnitProt.ws' will often drop the query IDs. To address this, the query result contains an extra 'QueryID' column when 'chunksize=1', but not when it is set to a different value than 1.

The getParalogs function is similar but it uses biomaRt's paralogs instead of UNIREF clusters.

Usage

getUniprotIDs(taxId = 9606, kt = "ENSEMBL", keys, seq_cluster = "UNIREF90", chunksize=20)
getUniprotIDs(taxId = 9606, kt = "ENSEMBL", keys, seq_cluster = "UNIREF90", chunksize=20)

Arguments

`taxId`	An NCBI taxonomy ID
`kt`	Should be either "ENSEMBL" or "UNIPROTKB".
`keys`	Query IDs.
`seq_cluster`	Which cluster to use. Should be one of 'UNIREF100', 'UNIREF90', 'UNIREF50'.
`chunksize`	Queries are done in batches, this parameter sets the size of each batch.

Value

Returns a list of data.

Author(s)

Thomas Girke

Examples

	 
		 keys <- c("ENSG00000145700", "ENSG00000135441", "ENSG00000120071", "ENSG00000120088", "ENSG00000185829", "ENSG00000185829", "ENSG00000185829", "ENSG00000238083", "ENSG00000012061", "ENSG00000104856", "ENSG00000104936", "ENSG00000117877", "ENSG00000130202", "ENSG00000130202", "ENSG00000142252", "ENSG00000189114", "ENSG00000234906") 
		 res_list100 <- getUniprotIDs(taxId=9606, kt="ENSEMBL", keys=keys, seq_cluster="UNIREF100") 
	

keys <- c("ENSG00000145700", "ENSG00000135441", "ENSG00000120071", "ENSG00000120088", "ENSG00000185829", "ENSG00000185829", "ENSG00000185829", "ENSG00000238083", "ENSG00000012061", "ENSG00000104856", "ENSG00000104936", "ENSG00000117877", "ENSG00000130202", "ENSG00000130202", "ENSG00000142252", "ENSG00000189114", "ENSG00000234906") 
		 res_list100 <- getUniprotIDs(taxId=9606, kt="ENSEMBL", keys=keys, seq_cluster="UNIREF100")

processDrugage

Description

Download Drug Age data from genomics.senescence.info/drugs. Process the data and write it out as a TSV spreadsheet.

Usage

processDrugage(drugagefile=file.path(config$resultsPath,"drugage_id_mapping.xls"), redownloaddrugage=TRUE,config=genConfig()) 
processDrugage(drugagefile=file.path(config$resultsPath,"drugage_id_mapping.xls"), redownloaddrugage=TRUE,config=genConfig())

Arguments

`drugagefile`	The name of the output file.
`redownloaddrugage`	If true, download the data file. Otherwise assume the file is already downloaded.
`config`	General configuration. See `genConfig`.

Value

Output is written to drugagefile.

Author(s)

Thomas Girke

Examples


	tryCatch({
		config = genConfig(chemblDbPath= 
									system.file("extdata", "chembl_sample.db", package="drugTargetInteractions"))
		processDrugage("druage_id_mapping.xls",TRUE,config)
	},
	error=function(e){
			message("Failed to run processDrugage(), please try again later")
		}
	)
tryCatch({
		config = genConfig(chemblDbPath= 
									system.file("extdata", "chembl_sample.db", package="drugTargetInteractions"))
		processDrugage("druage_id_mapping.xls",TRUE,config)
	},
	error=function(e){
			message("Failed to run processDrugage(), please try again later")
		}
	)

runDrugTarget_Annot_Bioassay

Description

Meta-function to obtain in one step both drug-target annotation and bioassay data.

Usage

runDrugTarget_Annot_Bioassay(res_list, up_col_id="ID", ens_gene_id,  cmpid_file=file.path(config$resultsPath,"cmp_ids.rds") ,config=genConfig(), ...) 
runDrugTarget_Annot_Bioassay(res_list, up_col_id="ID", ens_gene_id,  cmpid_file=file.path(config$resultsPath,"cmp_ids.rds") ,config=genConfig(), ...)

Arguments

`res_list`	Object obtained from `getUniprotIDs` function.
`up_col_id`	Column name in `data.frames` of `res_list` containing uniprot IDs, usually one of: 'ID', 'ID_up_sp' or 'ID_up_sp_tr'.
`ens_gene_id`	Named character vector with ENSEMBL gene IDs in name slot and gene symbols or other ID type in value slot
`cmpid_file`	Path to CMP ID mapping file, often named `cmp_ids.rds`.
`config`	General configuration. See `genConfig`.
`...`	Slot to pass on additional arguments.

Value

List with two components each containing a data.frame. The first one (Annotation) contains drug-target annotation data, and the second one (Bioassay) contains drug-target bioassay data.

Author(s)

Thomas Girke

References

References to be added...

Examples


	config = genConfig(chemblDbPath= 
									system.file("extdata", "chembl_sample.db", package="drugTargetInteractions"),
							  resultsPath = 
									system.file("extdata", "results", package="drugTargetInteractions"))

	## (1) Translate gene symbols to ENSEMBL gene IDs
	ensembl_gene_id <- c("ENSG00000001626", "ENSG00000168748")
	idMap <- getSymEnsUp(EnsDb="EnsDb.Hsapiens.v86", ids=ensembl_gene_id, idtype="ENSEMBL_GENE_ID")
	ens_gene_id <- idMap$ens_gene_id


	## (2a) Retrieve UniProt IDs with both IDMs and SSNN paralogs
	queryBy <- list(molType="gene", idType="ensembl_gene_id", ids=names(ens_gene_id))
	 
		#this function is slow and requires a network connection
		res_list <- getParalogs(queryBy)
	
	

	## (3) Obtain Drug-Target Annotation and Bioassay Data 
	drug_target_list <- runDrugTarget_Annot_Bioassay(res_list=res_list, 
											up_col_id="ID_up_sp", ens_gene_id,config=config ) 

config = genConfig(chemblDbPath= 
									system.file("extdata", "chembl_sample.db", package="drugTargetInteractions"),
							  resultsPath = 
									system.file("extdata", "results", package="drugTargetInteractions"))

	## (1) Translate gene symbols to ENSEMBL gene IDs
	ensembl_gene_id <- c("ENSG00000001626", "ENSG00000168748")
	idMap <- getSymEnsUp(EnsDb="EnsDb.Hsapiens.v86", ids=ensembl_gene_id, idtype="ENSEMBL_GENE_ID")
	ens_gene_id <- idMap$ens_gene_id


	## (2a) Retrieve UniProt IDs with both IDMs and SSNN paralogs
	queryBy <- list(molType="gene", idType="ensembl_gene_id", ids=names(ens_gene_id))
	 
		#this function is slow and requires a network connection
		res_list <- getParalogs(queryBy)
	
	

	## (3) Obtain Drug-Target Annotation and Bioassay Data 
	drug_target_list <- runDrugTarget_Annot_Bioassay(res_list=res_list, 
											up_col_id="ID_up_sp", ens_gene_id,config=config )

transformTTD

Description

Integration with Therapeutic Target Database (TTD). This function downloads a data file from idrblab.org and returns it as a data frame.

Usage

transformTTD(ttdfile=file.path(config$downloadPath,"TTD_IDs.txt"), redownloadTTD=TRUE,config=genConfig()) 
transformTTD(ttdfile=file.path(config$downloadPath,"TTD_IDs.txt"), redownloadTTD=TRUE,config=genConfig())

Arguments

`ttdfile`	The name of the output file to write the downloaded file to.
`redownloadTTD`	If true, data file will be downloaded again. If false, we assume the file already exists at `ttdfile`.
`config`	General configuration. See `genConfig`.

Value

Returns a data frame with TTD data in it.

Author(s)

Thomas Girke

Examples

		ttd=tryCatch(
			transformTTD(),
			error=function(e){
				message("Failed to download TTD file, please try again later")
			}
		)
ttd=tryCatch(
			transformTTD(),
			error=function(e){
				message("Failed to download TTD file, please try again later")
			}
		)

Package 'drugTargetInteractions'

Help Index

Drug-Target Interactions

Description

Details

Author(s)

cmpIdMapping

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

downloadChemblDb

Description

Usage

Arguments

Value

Author(s)

Examples

downloadUniChem

Description

Usage

Arguments

Value

Author(s)

References

See Also

Examples

drugTargetAnnot

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

drugTargetAnnotTable

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

drugTargetBioactivity

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

genConfig

Description

Usage

Arguments

Value

Author(s)

Examples

getDrugTarget

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

getParalogs

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

Gene to Protein ID Mappings

Description

Usage